5/13/25: UI Automation for controlling apertures and getting grid names will now try to open the needed panel in the lower right of the TEM UI instead of changing workset tabs. The default is now to monitor C2 aperture on Titan scopes when possible.
5/7/25: Added option in Navigator Realign setup dialog to apply setting for treatment of image shift to Realign to Item run from Navigator dialog or menu.
5/5/25: Added UI Automation code to control beam stop on Thermo which works on some scopes (Windows 10 and not Windows 7?).
5/5/25: Switched to having separate plugins for connecting to DE camera with API1 or API2; the UseAPI2forDE property is irrelevant with the API2 plugin.
4/7/25: Enabled dynamic focus to work with CL3 in LM on JEOL; fixed dynamic focus and probably some other problems when partial STEM scans are being returned. This applies to TVIPS STEM, and also to STEM on Thermo through UTAPI, where the ramp will done from SerialEM instead of FocusRamper.
3/27/25: Made Refine ZLP detect a transition from black to white, i.e., the slit entering rather than leaving the field.
3/26/25: Added option to skip center of pattern in multishot on hex grid.
3/25/25: Added option to track in a dose-symmetric series when the tilt from the other side exceed a specified amount.
3/25/25: Added dialog for setting acquisition parameters for CTF-based coma and astigmatism routines, including new options to specify frame alignment and do initial focus measurement with Focus area.
3/25/25: Made CTF-based astigmatism and coma routines switch between Ctffind and Ctfplotter for most kinds of errors, in case the other method works better.
3/23/25: Allowed the "Use map hole vectors" option in Acquire at Items to be set and have an effect when running a script as the main action.
3/23/25: Added calibration for saving an intensity at parallel illumination that can be returned to with a script command.
3/23/25: Added ability to map Ctrl F1-F10 to run specific scripts.
3/18/25: For Titan microscopes (UseIlluminatedArea property set to 1) with UTAPI scripting control of apertures, it will monitor the C2 aperture size and scale intensity values in tables automatically. With non-UTAPI aperture control, it will find out the size when a relevant calibration is done and scale automatically when the aperture is changed from SerialEM.
3/17/25: Added hot key Ctrl-Shift M to start/stop a continuous movie through the stack window used for tilt series and other stacks.
3/13/25: Allowed the center of the pattern for the calibrate coma versus IS pattern to be moved with the marker point.
3/13/25: Added separate beam tilt for autofocusing in LM.
3/13/25: Expanded One-line scripts from 5 to 10.
3/13/25: Moved Set C2 Aperture Size from Calibration to Tasks menu.
3/3/25: Added ability to set the multishot IS vectors automatically from hole vectors of the first map loaded from a grid.
3/3/25: Made IS vectors for multishot and adjusting transform be saved with multigrid settings for individual grids, and added option to take IS vectors from these settings.
2/20/25: When running Refine ZLP from Acquire at Items, it is now possible to specify that different energy ranges should be tried upon failure in Low Dose mode, and that failure should not generate an error. The script command has similar options.
2/20/25: Changed multishot display after combining to show boundaries around all combined points and to draw either boxes at acquire areas or triangles at holes being skipped.
2/20/25: Consolidated all the options about which area to use for tasks in Low Dose into a new dialog and eliminated the menu entries for them.
1/23/25: Made multigrid allow having hole vectors on just the first map.
12/31/24: Added routine to refine alignment after realigning to reloaded grid using correlations between medium-mag images and scaled-up portions of the grid map. A property can be added to make options show up in the multigrid dialog.
12/17/24: Rearranged microscope status panel.
12/17/24: Added "Eucen Focus" button to Align & Focus panel to set focus to the calibrated standard focus.
12/17/24: The NanumGothicCoding-Regular.ttf file will be sought in C:\Program Files\SerialEM and C:\ProgramData\SerialEM as well as in the executable directory, so one copy can be placed in one of those folders to support multiple versions.
11/17/24: Added support for electron dose modulator from IDES and made the relevant setting part of Low Dose parameters.
11/4/24: Added ability to open secondary log windows; added button to multigrid dialog to open logs from runs on a grid and fixed Clear button.
10/30/24: Automated the Step To and Adjust IS procedure to use cross-correlation or hole centering, and made it able to take preview montages so it can work closer to the Record mag.
10/30/24: Added routine and script command to find one hole and optionally center on it in an image with one or a few holes.
10/30/24: Made the routine that automatically measures View shift offset able to align in two mag steps when the mag range exceeds 20-fold.
10/30/24: Added script command and menu item to take a 3x3 Prescan montage with Preview in Low Dose, without setting up montaging.
10/30/24: Added ability to take montages with Preview in Low Dose.
10/30/24: Added property to specify refined pixel size at a mag to be used in file headers and mdoc files, to avoid inconsistencies between pixel sizes used within SerialEM.
10/18/24: Started saving states to be set in Navigator file.
9/21/24: Added options to autocontouring to make one polygon at a point clicked with the mouse and to find contours within a polygon subarea.
8/18/24: Added ability to define position of Focus and Trial areas with a line drawn anywhere in the image.
8/7/24: Made it possible to set different Focus area positions for different grids in multi-grid routine.
8/7/24: Added script command and interactive way to run hole finding and combining on a range of maps in the Navigator table.
8/7/24: Added script command and menu item to load all grid maps from a multigrid session or from a single Navigator file.
7/29/24: Added ability to set lenses with free lens control for a low dose area.
7/9/24: Added option to have tilt axis offset set automatically with lateral offset from fine eucentricity.
6/25/24: Added property to enable using the multiple grid operations with one grid and no autoloader, fixed some more problems.
6/12/24: Added dialog and procedures for running operations on multiple grids.
6/11/24: Add script command to set debug output, allowed aperture commands to take words starting with c or o for condenser or objective.
5/18/24: Added entry in Camera Setup dialog to set a tilt offset for STEM dynamic focusing.
4/18/23: Allowed hexadecimal values (starting with 0x) to be entered in script commands when an integer is expected, making it easier to set flag values.
4/16/24: Added routine to realign to a reloaded grid and transform Navigator items to a new registration.
4/12/24: Made montage fitting to an area try Search as well as View in Low Dose when there are too many pieces; made full montage use current area in Low Dose mode if it is View or Search and has a much larger pixel size.
3/19/24: Added ability to get early return from OneView type cameras and to get immediate early return instead of waiting for exposure to end.
2/29/24: Split the View/Search defocus and shift offset controls into two rows and added Auto buttons to find the shift offsets automatically.
2/17/24: To try a narrower font being considered as the default monospaced font, place NanumGothicCoding-Regular.ttf (from Testing-4.2 download directories) in SerialEM executable directory.
2/17/24: Added option to write logs as RTF files to preserve the formatting.
2/16/24: Added routine for measuring View or Search shift offsets using correlations between images at different mags; added script command for running this and other for manipulating these offsets.
2/16/24: Revised colors available; defined default colors for errors, warning, verbose and debug output, and user-inserted text, with properties to set these, and applied some formatting to calibration listings.
2/12/24: Added option to Navigator window to show item numbers in first column.
2/12/24: Made file choosers start in the current directory, changed current directory to that of chosen file, saved current directory in settings and set it when loading settings. This does not apply to settings and script-related files, which consistently default to the current settings directory.
2/10/24: Reformatted scope control panel for clearer organization.
2/4/24: Added ability to set text colors and type styles in log window and a script command to set the color and style for the next output; SEMMessageBox outputs will be red.
2/4/24: Put argument list summary from script help file on the completions line of a script editor when completion character is typed within or at end of complete command.
1/29/24: Added cryptic checkbox to show index numbers before names in the state dialog table.
1/25/24: Added ability to do third round of Realign to Item with scaled-up extract from lower mag map.
1/25/24: Allowed Step To & Adjust procedure to concatenate the transformation between mag 1 and mag 2 with a refining transform between mag 2 and mag 3 to give a transformation directly from mag 1 to mag 3.
1/19/24: Added ability to transform an image to match one at another mag, and to align between images at differents mags, with script commands for these operations.